Identification and Mapping of Eastern Filbert Blight Resistance Quantitative Trait Loci in European Hazelnut Using Double Digestion Restriction Site Associated DNA Sequencing

Abstract

<jats:p>European hazelnut (<jats:italic>Corylus avellana</jats:italic> L.) is an economically important edible nut producing species, which ranked sixth in world tree nut production in 2016. European hazelnut production in the United States is primarily limited to the Willamette Valley of Oregon, and currently nonexistent in the eastern United States because of the presence of a devastating endemic disease, eastern filbert blight (EFB) caused by <jats:italic>Anisogramma anomala</jats:italic> (Peck) E. Muller. The primary commercial means of control of EFB to date is through the development and planting of genetically resistant european hazelnut cultivars, with an <jats:italic>R</jats:italic>-gene introduced from the obsolete, late-shedding pollinizer ‘Gasaway’. Although the ‘Gasaway’ resistance source provides protection against EFB in the Pacific northwestern United States (PNW), recent reports have shown that it is not effective in parts of the eastern United States. This may be in part because the identification and selection of ‘Gasaway’ and ‘Gasaway’-derived cultivars occurred in an environment (PNW) with limited genetic diversity of <jats:italic>A. anomala</jats:italic>. The objectives of the current research were to develop a genetic linkage map using double digestion restriction site associated DNA sequencing (ddRADseq) and identify quantitative trait loci (QTL) markers associated with EFB resistance from the resistant selection Rutgers H3R07P25 from southern Russia. A mapping population composed of 119 seedling trees was evaluated in a geographic location (New Jersey) where the EFB fungus is endemic, exhibits high disease pressure, and has a high level of genetic diversity. The completed genetic linkage map included a total of 2217 markers and spanned a total genetic distance of 1383.4 cM, with an average marker spacing of 0.65 cM. A single QTL region associated with EFB resistance from H3R07P25 was located on european hazelnut linkage group (LG) 2 and was responsible for 72.8% of the phenotypic variation observed in the study. Based on its LG placement, origin, and disease response in the field, this resistance source is different from the ‘Gasaway’ source located on LG6. The current results, in combination with results from previous research, indicate that the H3R07P25 source is likely exhibiting resistance to a broader range of naturally occurring <jats:italic>A. anomala</jats:italic> isolates. As such, H3R07P25 will be important for the development of new european hazelnut germplasm that combines EFB resistance from multiple sources in a gene pyramiding approach. Identification of EFB resistance in high disease pressure environments representing a diversity of <jats:italic>A. anomala</jats:italic> populations is likely a requirement for identifying plants expressing durable EFB resistance, which is a precursor to the development of a commercially viable european hazelnut industry in the eastern United States.</jats:p>

New Simple Sequence Repeat Markers on Linkage Groups 2 and 7, and Investigation of New Sources of Eastern Filbert Blight Resistance in Hazelnut

“…The DNA sequences of a set of previously developed SSR markers on LG2 and LG7 (Table 2) were aligned with the 'Jefferson' genome (V2) assembled from PacBio sequences (Snelling et al, 2018). In addition, 28 double digest restriction site associated DNA sequencing (ddRAD-Seq) markers with positions from 2.57 to 24.76 cM on LG2 were aligned with the V2 'Jefferson' reference genome, of which RUCaS1_18603 and RUCaS1_14004 flanked the EFB resistance quantitative trait locus (QTL) in Rutgers University selection H3R07P25 from Holmskij, Russia (Honig et al, 2019). The alignment of the marker sequences with the V2 genome sequence identified contigs associated with the EFB resistance regions on these two LGs, and the contigs were mined for SSR motifs > 16 bp using the GMATo program (Wang et al, 2013).…”

“…Resistance in 'Ratoli' from Spain (Sathuvalli et al, 2011a), C. americana 'Rush', and interspecific hybrid 'Yoder #5' (Bhattarai et al, 2017b) was assigned to LG7. Resistance from OSU 759.010 from the Republic of Georgia and Rutgers University selection H3R07P25 from Holmskij, Russia was assigned to LG2 (Honig et al, 2019;Sathuvalli et al, 2011b). Sathuvalli et al (2010) reported that Moscow selections #2 and #27 were EFB resistant following greenhouse inoculation.…”

Diversity Assessment and DNA-Based Fingerprinting of Sicilian Hazelnut (Corylus avellana L.) Germplasm

“…SSRs have been proven to be highly effective tools in assessing genetic diversity also in Corylus avellana L. [ 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 ]. By these molecular markers, hazelnut germplasm collections have been fingerprinted, defining synonymies and homonymies [ 34 , 35 , 36 ], assessing genetic relationships and parentage [ 37 , 38 , 39 , 40 , 41 ], investigating the genetic structure of different populations comparing local cultivars and wild genotypes [ 29 , 32 , 38 , 42 , 43 ], and developing genetic maps for association analysis [ 44 , 45 ]. More recently, single-nucleotide polymorphisms (SNPs) based on next-generation sequencing (NGS) have been utilized in hazelnut linkage maps [ 46 , 47 ] to assess the genetic diversity and to investigate the domestication history of European hazelnut [ 48 , 49 , 50 ].…”

New Sources of Eastern Filbert Blight Resistance and Simple Sequence Repeat Markers on Linkage Group 6 in Hazelnut (Corylus avellana L.)

“…On the other hand, resistance in ‘Ratoli’ from Spain, C. americana ‘Rush’ from Pennsylvania and interspecific hybrid ‘Yoder #5’ from Ohio was assigned to a region on LG7 ( Sathuvalli et al, 2011a ; Bhattarai et al, 2017a ). Resistance in selection OSU 759.010 from the Republic of Georgia and Rutgers University selection H3R07P25 from southern Russia was assigned to a region on LG2 ( Sathuvalli et al, 2011b ; Honig et al, 2019 ). Additional sources of EFB resistance have been identified, including Moscow #26 ( Sathuvalli et al, 2010 ), C. heterophylla ‘Ogyoo’ ( Coyne et al, 1998 ), and interspecific hybrid ‘Estrella #1’ ( Chen et al, 2007 ), as well as germplasm collected in Russia, Crimea and Poland ( Molnar et al, 2007 ; Capik et al, 2013 ; Leadbetter et al, 2016 ).…”